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pcmsolver

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  1. :orphan:
  2.  
  3.  
  4. .. index:: *PCMSOL
  5. .. _*PCMSOL:
  6.  
  7. ========
  8. \*PCMSOL
  9. ========
  10.  
  11. PCMSolver module configuration directives.
  12.  
  13. General information on the PCM can be found in :cite:`Tomasi2005`.
  14. Details on the module can be found `here <http://pcmsolver.github.io/pcmsolver-doc/>`_
  15. The module source code is freely available under the LGPLv3 license `on this URL <https://github.com/PCMSolver/pcmsolver>`_
  16.  
  17. There are two ways of providing input to the PCMSolver module:
  18.  
  19. 1. by means of an additional input file, parsed by the `pcmsolver.py` script;
  20. 2. by means of a special section in the DIRAC input.
  21.  
  22. Method 1 is more flexible: all parameters that can be modified by the user are available.
  23. Method 2 just gives access to the core parameters. We will here describe Method 2, for a description
  24. of Method 1 refer to the `PCMSolver input documentation <http://pcmsolver.github.io/pcmsolver-doc/_input_description.html>`_
  25. Examples of both methods are given in the PCM tutorial section.
  26. All keywords expecting a numerical value are intended to be in Angstrom. The module will perform conversion
  27. to atomic units internally.
  28.  
  29. .. warning:: Do **NOT** truncate keyword values to six characters. It will result in a crash with an obscure error message.
  30.  
  31. .. warning:: Some keywords can be set but won't have any effect on the module as their respective functionality is not in the released version of PCMSolver.
  32.  
  33. **Cavity directives**
  34. =====================
  35.  
  36. The generating spheres for the cavity are obtained by centering spheres on the atoms making up the
  37. molecule. Radii are automatically selected from a built-in set and are scaled by 1.2.
  38. For a finer control over the cavity creation details use Method 1.
  39.  
  40. .. index:: .CAVTYP
  41. .. _PCMSOL_.CAVTYP:
  42.  
  43. .CAVTYP
  44. -------
  45.  
  46. The type of the cavity. Completely specifies type of molecular surface and its discretization.
  47. Allowed values are GEPOL and RESTART.
  48. If RESTART is given, teh module will read the file specified by the RESTAR keyword
  49. and create a GePol cavity from that. Default::
  50.  
  51.   .CAVTYP
  52.   GEPOL
  53.  
  54. .. index:: .PATCHL
  55. .. _PCMSOL_.PATCHL:
  56.  
  57. .PATCHL
  58. -------
  59.  
  60. .. warning:: not available in the current release of the module.
  61.  
  62. .. index:: .COARSI
  63. .. _PCMSOL_.COARSI:
  64.  
  65. .COARSI
  66. -------
  67.  
  68. .. warning:: not available in the current release of the module.
  69.  
  70. .. index:: .AREATS
  71. .. _PCMSOL_.AREATS:
  72.  
  73. .AREATS
  74. -------
  75.  
  76. Average area of the surface partition for the GePol cavity. Default::
  77.  
  78.   .AREATS
  79.   0.3
  80.  
  81. .. index:: .MINDIS
  82. .. _PCMSOL_.MINDIS:
  83.  
  84. .MINDIS
  85. -------
  86.  
  87. .. warning:: not available in the current release of the module.
  88.  
  89. .. index:: .DERORD
  90. .. _PCMSOL_.DERORD:
  91.  
  92. .DERORD
  93. -------
  94.  
  95. .. warning:: not available in the current release of the module.
  96.  
  97. .. index:: .NOSCAL
  98. .. _PCMSOL_.NOSCAL:
  99.  
  100. .NOSCAL
  101. -------
  102.  
  103. If present the radii for the spheres will **not** be scaled by 1.2. Radii are scaled by default.  
  104.  
  105. .. index:: .RADIIS
  106. .. _PCMSOL_.RADIIS:
  107.  
  108. .RADIIS
  109. -------
  110.  
  111. The set of built-in radii to be used. Allowed values are BONDI and UFF.
  112. Refer to the `PCMSolver input documentation <http://pcmsolver.github.io/pcmsolver-doc/_input_description.html>`_
  113. for further details about the radii sets. Default::
  114.  
  115.   .RADIIS
  116.   BONDI
  117.  
  118. .. index:: .RESTAR
  119. .. _PCMSOL_.RESTAR:
  120.  
  121. .RESTAR
  122. -------
  123.  
  124. The name of the `.npz` file to be used for the GePol cavity restart.
  125.  
  126. .. index:: .MINRAD
  127. .. _PCMSOL_.MINRAD:
  128.  
  129. .MINRAD
  130. -------
  131.  
  132. Minimal radius for additional spheres not centered on atoms. An arbitrary big value is equivalent
  133. to switching off the use of added spheres. By default, no spheres not centered on atoms are added. Default::
  134.  
  135.   .MINRAD
  136.   100.0
  137.  
  138. **Solver directives**
  139. =====================
  140.  
  141. .. index:: .SOLVER
  142. .. _PCMSOL_.SOLVER:
  143.  
  144. .SOLVER
  145. -------
  146.  
  147. Type of solver to be used. All solvers are based on the Integral Equation Formulation of
  148. the Polarizable Continuum Model:
  149.  
  150. * IEFPCM. Collocation solver for a general dielectric medium;
  151. * CPCM. Collocation solver for a conductor-like approximation to the dielectric medium.
  152.  
  153. .. index:: .SOLVNT
  154. .. _PCMSOL_.SOLVNT:
  155.  
  156. .SOLVNT
  157. -------
  158.  
  159. Specification of the dielectric medium outside the cavity. This keyword **must always** be
  160. given a value. Allowed values are:
  161.  
  162. * WATER              
  163. * METHANOL                                    
  164. * ETHANOL                                  
  165. * CHLOROFORM                                  
  166. * METHYLENECHLORIDE                          
  167. * 1,2-DICHLOROETHANE                        
  168. * CARBON TETRACHLORIDE                        
  169. * BENZENE                                      
  170. * TOLUENE                                  
  171. * CHLOROBENZENE                              
  172. * NITROMETHANE                              
  173. * N-HEPTANE                                  
  174. * CYCLOHEXANE                                
  175. * ANILINE                                  
  176. * ACETONE                                    
  177. * TETRAHYDROFURANE                              
  178. * DIMETHYLSULFOXIDE                            
  179. * ACETONITRILE                                
  180. * EXPLICIT
  181.  
  182. For further details on the dielectric properties of the available built-in solvents refer to the
  183. `PCMSolver input documentation <http://pcmsolver.github.io/pcmsolver-doc/_input_description.html>`_
  184. If the solvent name given is different from Explicit any other settings in the Green's function
  185. section will be overridden by the built-in values for the solvent specified.
  186. Solvent = Explicit, triggers parsing of the Green's function directives.
  187.  
  188. .. index:: .EQNTYP
  189. .. _PCMSOL_.EQNTYP:
  190.  
  191. .EQNTYP
  192. -------
  193.  
  194. .. warning:: not available in the current release of the module.
  195.  
  196. .. index:: .CORREC
  197. .. _PCMSOL_.CORREC:
  198.  
  199. .CORREC
  200. -------
  201.  
  202. Correction, :math:`k` for the apparent surface charge scaling factor in the CPCM solver
  203. :math:`f(\varepsilon) = \frac{\varepsilon - 1}{\varepsilon + k}`. Default::
  204.  
  205.   .CORREC
  206.   0.0
  207.  
  208. .. index:: .PROBER
  209. .. _PCMSOL_.PROBER:
  210.  
  211. .PROBER
  212. -------
  213.  
  214. Radius of the spherical probe approximating a solvent molecule. Used for generating the
  215. solvent-excluded surface (SES) or an approximation of it. Overridden by the built-in value
  216. for the chosen solvent. Default::
  217.  
  218.   .PROBER
  219.   1.0
  220.  
  221. **Green's function directives**
  222. ===============================
  223.  
  224. If solvent is Explicit, **both** the Green's function inside and outside
  225. must be specified.
  226. The Green's function inside will always be the vacuum, while the
  227. Green's function outside might vary. Currently, only isotropic uniform dielectrics
  228. are implemented.
  229.  
  230. .. index:: .GINSID
  231. .. _PCMSOL_.GINSID:
  232.  
  233. .GINSID
  234. -------
  235.  
  236. Type of Green's function inside the cavity. Default::
  237.  
  238.   .GINSID
  239.   VACUUM
  240.  
  241. .. index:: .GOUTSI
  242. .. _PCMSOL_.GOUTSI:
  243.  
  244. .GOUTSI
  245. -------
  246.  
  247. Type of Green's function inside the cavity. Default::
  248.  
  249.   .GINSID
  250.   UNIFORMDIELECTRIC
  251.  
  252. .. index:: .EPSILO
  253. .. _PCMSOL_.EPSILO:
  254.  
  255. .EPSILO
  256. -------
  257.  
  258. Static dielectric permittivity for the medium outside the cavity. Default::
  259.  
  260.   .EPSILO
  261.   1.0

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